For those interested, I did a write up about these problems and a few others, as well as possible solution. You can find it at my blog.
@JoshPetrie hit a lot of it on the nose, but I'll add a little to it as well.
Some friends and I a while back wanted to make a real MMORTS and went through the process of building a general game design outline that included features and a story and a few other things, and I can say from experience, transporting an RTS to a persistent state MMO presents a lot of difficult challenges for the genre.
For example, what would it mean to be offline? How does an entire civilization go offline? And what is to stop players from logging off when they are about to be rushed by another player? What happens to the land you own when you are offline? Are your buildings still there? Can people trade with you? Attack you?
What are the persistent goals? What is the point of the game in the long term? Build a big army? Build a civilization? For what purpose are you doing this? To fight other people? Where? How?
What happens if all of your civilization is destroyed? What does that mean? Do you revive? Do you have to start over? That would probably be frustrating.
What stops veterans with huge civilizations from destroying new players? What is a new player? Does the world just constantly expand? How much land do you get? When you conquer other players, do you get their land?
And there are a lot more questions just like these listed that crop up in taking an RTS to a persistent state. And that doesn't even touch on the MMO aspects and issues that crop up there. RTS, as the genre is now, is not made for a persistent state MMO environment.
Now, I will tell you, we came up with solutions for most of the above, so it isn't impossible. In fact, I would still be interested in some day seeing if I could get this to work. If anyone is interested in the solutions to some of these, I can do a write-up outside of this answer if you leave a comment. This answer, however, is long enough as it is...